PDBsum entry 6w2d

Viral protein

PDB id: 6w2d

Contents

Protein chains

1352 a.a.

1283 a.a.

292 a.a.

68 a.a.

37 a.a.

77 a.a.

63 a.a.

315 a.a.

336 a.a.

299 a.a.

PDB id:

6w2d

Name:

Viral protein

Title:

Structures of capsid and capsid-associated tegument complex inside the epstein-barr virus

Structure:

Major capsid protein. Chain: j, k, n, o, p. Synonym: mcp. Capsid vertex component 1. Chain: v. Synonym: cvc1. Capsid vertex component 2. Chain: w, x. Synonym: cvc2.

Source:

Epstein-barr virus (strain b95-8). Hhv-4. Organism_taxid: 10377. Strain: b95-8. Strain: b95-8

Authors:

W.Liu,Y.X.Cui,C.Y.Wang,Z.H.Li,D.Y.Gong,X.H.Dai,G.Q.Bi,R.Sun,Z.H.Zhou

Key ref:

W.Liu et al. (2020). Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Nat Microbiol, 5, 1285-1298. PubMed id: 32719506 DOI: 10.1038/s41564-020-0758-1

Date:

05-Mar-20 Release date: 15-Jul-20

Protein chains

P03226  (MCP_EBVB9) -  Major capsid protein from Epstein-Barr virus (strain B95-8)

Seq: 1381 a.a.

Struc: 1352 a.a.

Protein chain

P03226  (MCP_EBVB9) -  Major capsid protein from Epstein-Barr virus (strain B95-8)

Seq: 1381 a.a.

Struc: 1283 a.a.

Protein chain

P03222  (CVC1_EBVB9) -  Capsid vertex component 1 from Epstein-Barr virus (strain B95-8)

Seq: 507 a.a.

Struc: 292 a.a.

Protein chains

P03233  (CVC2_EBVB9) -  Capsid vertex component 2 from Epstein-Barr virus (strain B95-8)

Seq: 570 a.a.

Struc: 68 a.a.

Protein chains

P03186  (LTP_EBVB9) -  Large tegument protein deneddylase from Epstein-Barr virus (strain B95-8)

Seq: 3149 a.a.

Struc: 37 a.a.

Protein chains

P14348  (SCP_EBVB9) -  Small capsomere-interacting protein from Epstein-Barr virus (strain B95-8)

Seq: 176 a.a.

Struc: 77 a.a.

Protein chain

P14348  (SCP_EBVB9) -  Small capsomere-interacting protein from Epstein-Barr virus (strain B95-8)

Seq: 176 a.a.

Struc: 63 a.a.

Protein chain

P03187  (TRX1_EBVB9) -  Triplex capsid protein 1 from Epstein-Barr virus (strain B95-8)

Seq: 364 a.a.

Struc: 315 a.a.

Protein chain

P03187  (TRX1_EBVB9) -  Triplex capsid protein 1 from Epstein-Barr virus (strain B95-8)

Seq: 364 a.a.

Struc: 336 a.a.

Protein chains

P25214  (TRX2_EBVB9) -  Triplex capsid protein 2 from Epstein-Barr virus (strain B95-8)

Seq: 301 a.a.

Struc: 299 a.a.

Enzyme reactions

• Enzyme class 1: Chains J, K, N, O, P, v, w, x, Z, a, d, e, u, f, h, k, m, p, r: E.C.?
• Enzyme class 2: Chains y, z: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 3: Chains y, z: E.C.3.4.22.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/s41564-020-0758-1

Nat Microbiol 5:1285-1298 (2020)

PubMed id: 32719506

Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.

W.Liu, Y.Cui, C.Wang, Z.Li, D.Gong, X.Dai, G.Q.Bi, R.Sun, Z.H.Zhou.

ABSTRACT

As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.